How can Image files be properly organized?
No, you are right. When blender encounters files with the same name (regardless of where they are from), it assigns a .### to the end of the newly loaded file’s data block name (same is true of any data block being introduced into the blend file, actually). As you said, though, the filepath property of the images are still different, and the images are not equal. You can look at this property with:
&gt;&gt;&gt; bpy.data.images[“datablockname.png”].filepath